Using \clubpenalty10000 and \widowpenalty10000 is usually not the best way to avoid widow and club lines, especially with \flushbottom as they almost always make the constraints on page makeup impossible to achieve.
A typical example is a paragraph in which a last line has a couple of words which go over the page, by setting the penalties to 10000 you force TeX to send two lines over to the next page, thus leaving the current page short. Depending on whether there is any stretch glue on the page this leaves the page underfull, or at least unnecessarily loose.
Most paragraphs of more than a few lines could be broken to have a different number of lines so a better (although manual) solution is to add \looseness=-1 before the paragraph, so making TeX squeeze the paragraph into one less line so it all fits on the page, or set it to 1 so the paragraph has an extra line and send two lines over to the next page. (Note that you can do this with any paragraph on the page, it does not have to be the last paragraph, if no suitable line breaking can be found for that one).
Alternatively you can use \enlargethispage{\baselineskip} (usually for both pages on a double page spread) to squeeze an extra line onto the page.
These are manual corrections so not suitable for an automated printing of some database catalogue, where the penalty settings might be appropriate, but for a hand written book, the time taken to do a final page-breaking adjustment should be small compared to the time taken to actually write the text.
Classical TeX does not have a feedback from the page breaking to the linebreaking so this is most easily done via manual correction, although in luatex one could consider using the line and page breaking callbacks to automate this.
\makeatletter \newcommand*\mildraggedbottom{\def\@textbottom{\vskip\z@\@plus 12\p@ \relax}\let\@texttop\relax} \makeatother. But I’m not sure this is a good idea. – GuM Jul 04 '16 at 23:38\enlargethispageis the only feasible solution. – egreg Jul 04 '16 at 23:38\raggedbottom. (and yes, I commented raggedbottom ;)) – stack_horst Jul 06 '16 at 07:04